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Warn the user if trying to train with too few variants 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5776 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-06 17:47:58 +00:00
parent c2e8c460cb
commit d8a761bbbd
1 changed files with 3 additions and 0 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
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@ -32,6 +32,9 @@ public class VariantRecalibratorEngine {
} }
public GaussianMixtureModel generateModel( final List<VariantDatum> data ) { public GaussianMixtureModel generateModel( final List<VariantDatum> data ) {
if( data.size() < 1500 ) {
logger.warn("WARNING: Training with very few variant sites! Please check the model reporting PDF to ensure the quality of the model is reliable.");
}
final GaussianMixtureModel model = new GaussianMixtureModel( VRAC.MAX_GAUSSIANS, data.get(0).annotations.length, VRAC.SHRINKAGE, VRAC.DIRICHLET_PARAMETER, VRAC.PRIOR_COUNTS ); final GaussianMixtureModel model = new GaussianMixtureModel( VRAC.MAX_GAUSSIANS, data.get(0).annotations.length, VRAC.SHRINKAGE, VRAC.DIRICHLET_PARAMETER, VRAC.PRIOR_COUNTS );
variationalBayesExpectationMaximization( model, data ); variationalBayesExpectationMaximization( model, data );
return model; return model;